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Recent advances in high-resolution mass spectrometry and separation technologies are creating a revolution in proteomic data generation and biological inquiry. In step with these advancements comes a new generation of signal-processing and informatics platforms intended to comprehensively mine data for both protein identification and quantitation. In this talk, we discuss an open-source flexible platform for mining data from these new instruments. The platform contains three or more different quantitative pipelines, including traditional LC-MS/MS protein and peptide sequencing, LC-MS fingerprinting, and accurate mass and time (AMT) approaches. This system, described generally as the computational proteomics analysis system (CPAS), is the integration of numerous tools and data standards, most notably the suite of tools from the Institute of Systems Biology, the X!Tandem search engine, msInspect, the Labkey platform, and recently developed tools for the evaluation and identification of protein isoforms and variants, and integration of genomic information. The platform is design to be highly modifiable, allowing researchers to plug their own novel tools into the platform.